Analysis of variable sites between two complete South China tiger (Panthera tigris amoyensis) mitochondrial genomes

In order to investigate the mitochondrial genome of Panthera tigris amoyensis, two South China tigers (P25 and P27) were analyzed following 15 cymt-specific primer sets. The entire mtDNA sequence was found to be 16,957 bp and 17,001 bp long for P25 and P27 respectively, and this difference in length between P25 and P27 occurred in the number of tandem repeats in the RS-3 segment of the control region. The structural characteristics of complete P. t. amoyensis mitochondrial genomes were also highly similar to those of P. uncia. Additionally, the rate of point mutation was only 0.3% and a total of 59 variable sites between P25 and P27 were found. Out of the 59 variable sites, 6 were located in 6 different tRNA genes, 6 in the 2 rRNA genes, 7 in non-coding regions (one located between tRNA-Asn and tRNA-Tyr and six in the D-loop), and 40 in 10 protein-coding genes. COI held the largest amount of variable sites (9 sites) and Cytb contained the highest variable rate (0.7%) in the complete sequences. Moreover, out of the 40 variable sites located in 10 protein-coding genes, 12 sites were nonsynonymous.     

抗炎性细胞因子与抑郁症

细胞因子假说是关于抑郁症发病机理的重要假说,为探讨抑郁症的发病机理和临床治疗方法提供了新方向.细胞因子分为前炎性细胞因子和抗炎性细胞因子.前炎性细胞因子与抑郁症的发病密切相关,而抗炎性细胞因子可能具有抗抑郁的作用.本文着重综述抗炎性细胞因子与抑郁症的关系.抗炎性细胞因子如白介素10、白介素1受体拮抗剂、白介素4、白介素13、转化生长因子β和脂联素等,在抑郁症中表达下降;补充外源抗炎性细胞因子则具有一定的抗抑郁作用.抗炎性细胞因子可通过拮抗前炎性细胞因子的作用,并与MAPK信号通路、神经递质和糖皮质激素相互作用而参与到抑郁症中.抗抑郁药能使抗炎性细胞因子的表达上升,这可能是药物起效的机制之一.抗炎策略在抑郁症的治疗中有重要应用前景.     

刚毛柽柳S-腺苷甲硫氨酸合成酶(ThSAMS)基因的克隆及表达分析

通过对刚毛柽柳转录组分析,克隆获得了一条与S-腺苷甲硫氨酸合成酶(SAMS)基因同源性高的基因,命名为ThSAMS。序列分析结果表明:ThSASM基因全长cDNA为1185bp,编码394个氨基酸,编码蛋白相对分子质量为97.85kDa,理论等电点为5.02。通过生物信息学分析表明,ThSASM基因编码的氨基酸与其他物种SAMS基因编码的氨基酸具有很高的同源性,其中与枣的同源性最高,达95%。实时荧光定量PCR(quantitativereal-timePCR,qRT-PCR)分析表明,ThSASM表达受NaCl、聚乙二醇(PEG)和ABA处理做出应答,暗示ThSASM可能参与了刚毛柽柳对盐和干旱的胁迫应答,为进一步研究SAMS基因在植物胁迫应答中的功能及作用机制提供了参考依据。     

PSMD: An extensive database for pan‐species microsatellite investigation and marker development

Microsatellites are widely distributed throughout nearly all genomes which have been extensively exploited as powerful genetic markers for diverse applications due to their high polymorphisms. Their length variations are involved in gene regulation and implicated in numerous genetic diseases even in cancers. Although much effort has been devoted in microsatellite database construction, the existing microsatellite databases still had some drawbacks, such as limited number of species, unfriendly export format, missing marker development, lack of compound microsatellites and absence of gene annotation, which seriously restricted researchers to perform downstream analysis. In order to overcome the above limitations, we developed PSMD (Pan‐Species Microsatellite Database, http://big.cdu.edu.cn/psmd/ ) as a web‐based database to facilitate researchers to easily identify microsatellites, exploit reliable molecular markers and compare microsatellite distribution pattern on genome‐wide scale. In current release, PSMD comprises 678,106,741 perfect microsatellites and 43,848,943 compound microsatellites from 18,408 organisms, which covered almost all species with available genomic data. In addition to interactive browse interface, PSMD also offers a flexible filter function for users to quickly gain desired microsatellites from large data sets. PSMD allows users to export GFF3 formatted file and CSV formatted statistical file for downstream analysis. We also implemented an online tool for analysing occurrence of microsatellites with user‐defined parameters. Furthermore, Primer3 was embedded to help users to design high‐quality primers with customizable settings. To our knowledge, PSMD is the most extensive resource which is likely to be adopted by scientists engaged in biological, medical, environmental and agricultural research.     

A Bipartite Network-based Method for Prediction of Long Non-coding RNA–protein Interactions

As one large class of non-coding RNAs(nc RNAs), long nc RNAs(lncRNAs) have gained considerable attention in recent years. Mutations and dysfunction of lnc RNAs have been implicated in human disorders. Many lnc RNAs exert their effects through interactions with the corresponding RNA-binding proteins. Several computational approaches have been developed, but only few are able to perform the prediction of these interactions from a network-based point of view. Here,we introduce a computational method named lnc RNA–protein bipartite network inference(LPBNI). LPBNI aims to identify potential lnc RNA–interacting proteins, by making full use of the known lnc RNA–protein interactions. Leave-one-out cross validation(LOOCV) test shows that LPBNI significantly outperforms other network-based methods, including random walk(RWR)and protein-based collaborative filtering(Pro CF). Furthermore, a case study was performed to demonstrate the performance of LPBNI using real data in predicting potential lnc RNA–interacting proteins.     

少数民族林区可持续发展实证分析

本文对少数民族林区研究范畴进行了界定,通过运用AHP分析法构建可持续发展指标体系,对少数民族林区可持续发展指数和能力进行了分析,提出了少数民族林区可持续发展过程中出现的主要问题和可能影响可持续发展的各种因素。     

基于BP神经网络模型的全球森林土壤异养硝化过程N2O排放通量估算

N₂O作为重要的温室气体之一,对地球和人类都有很大的影响。为了深入探究对有机氮异养硝化作用及其产生N₂O过程的影响机制,完善全球N₂O通量估算模型,本研究采用Pearson相关性分析与广义可加模型(GAM)对全球135个样点有机氮异养硝化速率及其产生N₂O速率的影响因子进行分析,然后将主要影响因子作为BP神经网络的输入层来模拟全球森林土壤有机氮异养硝化速率及其产生N₂O速率的空间分布。结果显示,土壤pH和土壤C/N是影响有机氮异养硝化速率的主要因素,土壤C/N、土壤孔隙含水量(WFPS)以及土壤温度是影响有机氮异养硝化产生N₂O速率的主要因素。全球森林土壤异养硝化速率平均为0.4241(0.0014～0.689)μg N·g^-1·d^-1,异养硝化产生N₂O速率平均为0.2936(0.21～1.103)μg N₂O·kg^-1·d^-1     

Low Molecular Weight Heparin Ablates Lung Cancer Cisplatin-Resistance by Inducing Proteasome-Mediated ABCG2 Protein Degradation

Cancer side population (SP) cells, which are often referred to as cancer stem cells, are thought to be responsible for lung cancer chemotherapy resistance, and currently no drug can specifically target these cells. We hypothesize low-molecular-weight heparin (LMWH) may affect the biological properties of SP cells and could be used to clinically target these cells. To test this, SP cells were isolated from cisplatin (DDP)-resistant lung adenocarcinoma A549/DDP cells by flow cytometric sorting. Compared to non-SP cells, SP cells formed increased numbers of colonies in vitro, and had a 1000-fold increase in tumorigenicity in vivo. Proliferation and apoptosis assays demonstrated LMWH had no significant effect on lung SP cell proliferation or apoptosis. However, LMWH reduced lung SP cell colony formation ability and protein expression of the multidrug transporter, ABCG2, by FACS and western blot analyses without affecting its mRNA levels by RT-PCR. Consistently, immunohistochemistry stainings of ABCG2 in LMWH-treated tumor tissues were significantly reduced compared with those in controls. Further, we found proteasomal inhibitor MG132, but not lysosomal inhibitors leupeptin and pepstatin A, could restore ABCG2 protein levels in LMWH-treated SP cells. These suggest LMWH ablates lung SP cell chemoresistance by proteasome-mediated reduction of ABCG2 protein levels without affecting its mRNA levels. We also determined LMWH combined with cisplatin could overcome cisplatin-resistance and induced lung SP cells apoptosis both in vitro and in vivo. This study provides an experimental basis for using a combination of LMWH, which targets lung SP cells, with chemotherapy to improve lung cancer survival.     

土壤理化性质驱动烤烟根际细菌群落的组配及其共现性网络互作

【目的】解析土壤微生物在植物根际的组配机制对于认识和维护农田生态系统的稳定性至关重要。【方法】通过Illumina高通量测序和生物信息学分析方法明确了我国主要种植烟草生态区烤烟根际土壤细菌群落与土壤理化性质的互作关系。【结果】烤烟根际细菌类群主要为放线菌纲(Actinobacteria)、α-变形菌纲(Alphaproteobacteria)、γ-变形菌纲(Gammaproteobacteria)和嗜热油菌纲(Thermoleophilia)。细菌群落组成按生态区聚类,且样本空间距离和细菌群落相似度显著负相关。共现性网络分析表明,烤烟根际细菌群落间协同作用大于拮抗作用,武陵秦巴生态区、黄淮平原生态区、南岭丘陵生态区和沂蒙丘陵生态区细菌群落高度模块化,小单胞菌属(Micromonospora)为南岭丘陵生态区和黄淮生态区细菌共现性网络的网络中心,Bryobacter和气单胞菌属(Arenimonas)为南岭丘陵生态区细菌网络的模块核心,其菌群特性而非相对丰度决定了其在稳定细菌网络中的重要作用。冗余分析结果证实pH、有效铁、交换性镁和有效锰能显著影响烤烟根际细菌群落结构。【结论】烤烟根际细...     

ASPP2增强结肠癌HCT116细胞对奥沙利铂的化疗敏感性

为研究ASPP2对奥沙利铂诱导的结肠癌细胞系HCT116 p53+/+(野生型)凋亡及周期的影响.利用ASPP2（rAd-ASPP2）及p53腺病毒（rAd-p53）感染HCT116 p53+/+细胞,经奥沙利铂50 μmol/L诱导细胞凋亡及周期改变.Western印迹检测ASPP2及p53的表达水平;MTT法检测ASPP2腺病毒对奥沙利铂诱导的HCT116细胞活性的影响;Calcein/PI吸收试验检测细胞凋亡情况;流式细胞术分析细胞周期分布. 结果显示,ASPP2、p53共同过表达,或者ASPP2单独过表达均能增强奥沙利铂诱导的HCT116 p53+/+细胞增殖抑制,以及S期抑制并伴有细胞凋亡水平的升高;而无奥沙利铂诱导时,ASPP2对HCT116 p53+/+细胞的活性、细胞周期及细胞凋亡水平的影响无统计学意义. 上述结果表明,ASPP2能够增强奥沙利铂诱导HCT116 p53+/+细胞的增殖抑制、细胞周期抑制和细胞凋亡.